Genome-wide association study and transcriptome analysis dissect the genetic control of silique length in Brassica napus L.

Wang, Jia; Fan, Yueling; Lin, Mao; Qu, Cunmin; Lu, Kun; Li, Jiana; Liu, Liezhao

doi:10.1186/s13068-021-02064-z

Cited by 15 publications

(12 citation statements)

References 86 publications

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“…The WGCNA is an effective method to narrow down the range of candidate genes ( Schaefer et al., 2018 ). Recently, GWAS combined with WGCNA has been applied to identify the genes responsible for salt tolerance in maize, silique length in Brassica napus , and root growth dynamics in rapeseed ( Li et al., 2021 ; Ma et al., 2021 ; Wang et al., 2021 ). However, no study has used the GWAS and the WGCNA to explain the gene networks and molecular regulatory mechanisms that govern isoflavone regulation in soybean.…”

Section: Introductionmentioning

confidence: 99%

Identification of hub genes regulating isoflavone accumulation in soybean seeds via GWAS and WGCNA approaches

Azam

Zhang²,

Li³

et al. 2023

Front. Plant Sci.

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IntroductionIsoflavones are the secondary metabolites synthesized by the phenylpropanoid biosynthesis pathway in soybean that benefits human and plant health.MethodsIn this study, we have profiled seed isoflavone content by HPLC in 1551 soybean accessions grown in Beijing and Hainan for two consecutive years (2017 and 2018) and in Anhui for one year (2017).ResultsA broad range of phenotypic variations was observed for individual and total isoflavone (TIF) content. The TIF content ranged from 677.25 to 5823.29 µg g-1 in the soybean natural population. Using a genome-wide association study (GWAS) based on 6,149,599 single nucleotide polymorphisms (SNPs), we identified 11,704 SNPs significantly associated with isoflavone contents; 75% of them were located within previously reported QTL regions for isoflavone. Two significant regions on chromosomes 5 and 11 were associated with TIF and malonylglycitin across more than 3 environments. Furthermore, the WGCNA identified eight key modules: black, blue, brown, green, magenta, pink, purple, and turquoise. Of the eight co-expressed modules, brown (r = 0.68***), magenta (r = 0.64***), and green (r = 0.51**) showed a significant positive association with TIF, as well as with individual isoflavone contents. By combining the gene significance, functional annotation, and enrichment analysis information, four hub genes Glyma.11G108100, Glyma.11G107100, Glyma.11G106900, and Glyma.11G109100 encoding, basic-leucine zipper (bZIP) transcription factor, MYB4 transcription factor, early responsive to dehydration, and PLATZ transcription factor respectively were identified in brown and green modules. The allelic variation in Glyma.11G108100 significantly influenced individual and TIF accumulation.DiscussionThe present study demonstrated that the GWAS approach, combined with WGCNA, could efficiently identify isoflavone candidate genes in the natural soybean population.

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Section: Introductionmentioning

confidence: 99%

Identification of hub genes regulating isoflavone accumulation in soybean seeds via GWAS and WGCNA approaches

Azam

Zhang²,

Li³

et al. 2023

Front. Plant Sci.

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“…6 a). The negative correlation between oil and protein/sugar accumulation in seeds suggested that the ratio of OBs to cell size was highly positively correlated with oil content [ 19 , 38 – 40 ]. Comparing the SOCs of the overexpression and knockdown/knockout lines demonstrated that BnLPAT family genes are indispensable for seed oil accumulation in B. napus .…”

Section: Discussionmentioning

confidence: 99%

“…Furthermore, KEGG enrichment analysis showed that the DEGs involved in lipid metabolism might enhance oil biosynthesis in the overexpression lines while promoting oil degradation in the knockdown and knockout lines. In addition, in line with the increase in seed protein and sugar contents, the DEGs of the knockdown and knockout lines were significantly enriched in carbohydrate metabolism, glycan biosynthesis metabolism, and amino acid biosynthesis pathways, thus demonstrating that competitive relationships existed between amino acids/sugar and FA in the use of photosynthesis products [ 40 , 47 – 49 ].…”

Section: Discussionmentioning

confidence: 99%

Lysophosphatidic acid acyltransferase 2 and 5 commonly, but differently, promote seed oil accumulation in Brassica napus

Zhang

Yin

et al. 2022

Biotechnol Biofuels

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Background Increasing seed oil content (SOC) of Brassica napus has become one of the main plant breeding goals over the past decades. Lysophosphatidic acid acyltransferase (LPAT) performs an important molecular function by regulating the production of phosphatidic acid (PA), a key intermediate in the synthesis of membrane and storage lipids. However, the mechanism underlying the effect of LPAT on the SOC of B. napus remains unclear. Results In the present study, significant elevation of SOC was achieved by overexpressing BnLPAT2 and BnLPAT5 in B. napus. RNAi and CRISPR–Cas9 were also successfully used to knock down and knock out these two genes in B. napus where SOC significantly decreased. Meanwhile, we found an accumulation of lipid droplets and oil bodies in seeds of BnLPAT2 and BnLPAT5 overexpression lines, whereas an increase of sugar and protein in Bnlpat2 and Bnlpat5 mutant seeds. Sequential transcriptome analysis was further performed on the developing seeds of the BnLPAT2 and BnLPAT5 overexpression, knockdown, and knockout rapeseed lines. Most differentially expressed genes (DEGs) that were expressed in the middle and late stages of seed development were enriched in photosynthesis and lipid metabolism, respectively. The DEGs involved in fatty acid and lipid biosynthesis were active in the overexpression lines but were relatively inactive in the knockdown and knockout lines. Further analysis revealed that the biological pathways related to fatty acid/lipid anabolism and carbohydrate metabolism were specifically enriched in the BnLPAT2 overexpression lines. Conclusions BnLPAT2 and BnLPAT5 are essential for seed oil accumulation. BnLPAT2 preferentially promoted diacylglycerol synthesis to increase SOC, whereas BnLPAT5 tended to boost PA synthesis for membrane lipid generation. Taken together, BnLPAT2 and BnLPAT5 can jointly but differently promote seed oil accumulation in B. napus. This study provides new insights into the potential mechanisms governing the promotion of SOC by BnLPAT2 and BnLPAT5 in the seeds of B. napus.

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“…Finally, a dynamic tree cut algorithm was used to identify co-expression gene modules. This method can detect nested clusters and have been shown to better detect outliers [ 71 ]. The major parameters were defined with a minimum size cut-off of 30 genes and a threshold of 0.3 and a minimum size cut-off of 100 genes and a threshold of 0.99 for avoiding abnormal modules in dendrogram, on the biotic and hormonal data respectively.…”

Section: Methodsmentioning

confidence: 99%

Integrative systems biology analysis of barley transcriptome ─ hormonal signaling against biotic stress

et al. 2023

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Biotic stresses are pests and pathogens that cause a variety of crop diseases and damages. In response to these agents, crops trigger specific defense signal transduction pathways in which hormones play a central role. To recognize hormonal signaling, we integrated barley transcriptome datasets related to hormonal treatments and biotic stresses. In the meta-analysis of each dataset, 308 hormonal and 1232 biotic DEGs were identified respectively. According to the results, 24 biotic TFs belonging to 15 conserved families and 6 hormonal TFs belonging to 6 conserved families were identified, with the NF-YC, GNAT, and WHIRLY families being the most prevalent. Additionally, gene enrichment and pathway analyses revealed that over-represented cis-acting elements were recognized in response to pathogens and hormones. Based on the co-expression analysis, 6 biotic and 7 hormonal modules were uncovered. Finally, the hub genes of PKT3, PR1, SSI2, LOX2, OPR3, and AOS were candidates for further study in JA- or SA-mediated plant defense. The qPCR confirmed that the expression of these genes was induced from 3 to 6 h following exposure to 100 μM MeJA, with peak expression occurring between 12 h and 24 h and decreasing after 48 h. Overexpression of PR1 was one of the first steps toward SAR. As well as regulating SAR, NPR1 has also been shown to be involved in the activation of ISR by the SSI2. LOX2 catalyzes the first step of JA biosynthesis, PKT3 plays an important role in wound-activated responses, and OPR3 and AOS are involved in JA biosynthesis. In addition, many unknown genes were introduced that can be used by crop biotechnologists to accelerate barley genetic engineering.

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Genome-wide association study and transcriptome analysis dissect the genetic control of silique length in Brassica napus L.

Cited by 15 publications

References 86 publications

Identification of hub genes regulating isoflavone accumulation in soybean seeds via GWAS and WGCNA approaches

Identification of hub genes regulating isoflavone accumulation in soybean seeds via GWAS and WGCNA approaches

Lysophosphatidic acid acyltransferase 2 and 5 commonly, but differently, promote seed oil accumulation in Brassica napus

Integrative systems biology analysis of barley transcriptome ─ hormonal signaling against biotic stress

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